DNA evidence suggests the bonobo and common chimpanzee species effectively separated from each other fewer than one million years ago.[21][22] The chimpanzee line split from the last common ancestor shared with humans approximately six to seven million years ago. Because no species other than Homo sapiens has survived from the human line of that branching, both Pan species are the closest living relatives of humans and cladistically are equally close to humans.

Because the two species are not proficient swimmers, the formation of the Congo River 1.5–2 million years ago possibly led to the speciation of the bonobo. They live south of the river, and thereby were separated from the ancestors of the common chimpanzee, which live north of the river.